Halo Effect 2
by Sharp47
Summary: Less than a month after the battle of the Citadel Commander Shepard is killed while on a patrol but is revived by Cerberus a Pro human organization who want his help in investigating the disappearance of entire human colonies
1. Chapter 1

July 3rd 2583, Location Unknown

In the center of a dimly lit room a man sat in his chair smoking and drinking while looking out the observation deck at the star the station was very close to he took another drag from his cigarette and the woman that was close to the window spoke

"Shepard did everything right, More than we could have hoped for saving the citadel even saving the council humanity has the trust of the entire galaxy, and still its not enough" She turned and walked towards the man in the chair who spoke "Our sacrifices have earned the council's gratitude but Shepard remains our best hope" The woman spoke again "But there sending him to fight Geth, Geth!, we both now their not the real threat, the reapers are still out there"

"And its up to us to stop them" He exhaled blowing smoke "The council will never trust cerberus they'll never accept oure help even after everything we've accomplished but Shepard they'll follow him he's a leader a bloody icon, but he's just one man if we lose Shepard Humanity might well follow" The man in the chair put his cigarette in the ash tray and looked forward as he spoke "Then see to it we don't lose him" his cybernetic eyes focused on the star outside

In 2583 a rogue spectre named Saren Arterius and his army of Geth started a war against the UNSC culminating in the battle of the citadel with the UNSC Fifth fleet saving the council and destroying Saren's flagship Sovereign

In the aftermath of the battle Humanity despite not previously being a member of the Citadel was granted a seat on the council for its actions

But Commander Shepard claims that Sovereign was a Reaper and that they are a threat looming over the Galaxy

In order to calm fears Shepard has been sent in his ship to patrol the UEG border for any signs of geth activity

July 6th 2583, Border of the Terminus systems, UNSC Normandy

The Normandy exited the slipstream arriving at its destination activating its stealth systems as everyone went about their regular duties on the ship Navigator Pressley went towards the cockpit irritated by constantly having to patrol the same sectors over and over "We're wasting our time, four days up and down this sector and we haven't found any sign of geth activity" Joker shifted in his chair before speaking "Area's been hit four times in the past month somethings going on out here" Pressley was at one of the displays now and spoke "My moneys on slavers Terminus systems is crawling with them"

The Radar officer spoke "Picking up something on the long range scanner, unidentifed vessel looks like a cruiser"

"Doesn't match any known signatures"

"The Cruiser has changed course now on intercept trajectory" Pressley spoke up "Impossible the stealth systems are engaged there's no way a geth ship could possibly-" But Joker interrupted "Its not the Geth! Brace for evasive manouvers!" But try as he might the ship took a direct hit to one of the engines the biggest downside to the stealth systems is that while they are active the shields have to be taken offline, an explosion rocked the cockpit and Pressley was hit by it the Radar officer tried to help him but she was caught in another blast as all hell broke loose Joker tried to get the ship out of the system "Weapons down, Shields offline, Somebody get that fire out!" The ship took more and more damage as everyone scrambled for the escape pods trying to escape

Down on the lower deck Williams was running towards the end of the hall towards the main battery to see if Shepard was there he was and as Williams got close he spoke while putting his helmet on "Distress beacon is ready for launch" Williams did the same and spoke "Will we be getting any backup?" another explosion rocked the ship and Shepard replied "Doubt it all we can do is try and hold on"

"Joker's still in the cockpit he won't abandon ship, I'm not leaving either" Shepard turned towards her " I need you to get the crew to the escape pods i'll take care of Joker" Ashley tried to object but Shepard stopped her "Ashley go, Now" She starred at him for a second and spoke "Aye, Aye sir" Williams went to the last open pod and shuttled everyone in before entering herself Shepard activated the emergency beacon and the pods launched a second later

Shepard turned around and made his way towards the Upper deck and heard joker on the comm "Mayday! Mayday! Mayday! this is the UNSC Normandy we are under attack by an unknown enemy" As Shepard made his way into the remains of the CIC he felt his Mag boots activate seeing the debris all around him he slowly approached the cockpit and finally entered going over to Joker "Come on Joker we have to leave!"

"No I won't abandon the Normandy I can still save her"

"The Normandy's lost going down with the ship won't change that"

"Yeah okay help me up" Shepard retrieved Achilles data crystal and handed it to Joker as he helped him up and they made their way to the last escape pod but the unknown Cruiser fired again and Shepard barely got Joker inside before being knocked back by the weapon fire taking one last look Shepard activated the pods launch sequence hearing Joker yell "Shepard!" the Cruisers beam struck just behind Shepard blasting him and making him impact extremley hard against a bulkhead before being laucnhed into space as he tried to figure out what was going on Shepard noticed on his hud that his oxygen gear had failed he scrambled to get it functioning again but after a few short seconds everything went black and his body descended into the atmosphere of the planet below


	2. Chapter 2: Escape and discussions

Date Unknown, Location Unknown

Shepard didn't know what was happening his ears were ringing and he had a massive headache the last thing he remembered was being blown out of the Normandy and his Oxygen gear failing, He slowly opened his eyes and saw he was in a white room and faintly heard someone speak "-Reacting to outside stimuli" A woman walked over and looked down at him when he heard someone speak "Pulse rising quickly too quickly" The woman over him spoke "Dammit Wilson he's not ready give him the sedative" Shepard suddenly felt weak and his consciousness slowly slipped away and everything faded to black once again

Several hours later

"-pard, dammit Shepard wake up" An explosion rocked him and Shepard opened his eyes feeling alot of pain "Shepard you're scars aren't healed but you need to get out of there, there's a laser pistol in the locker get it" Shepard sat up and tried to stand but collapsed and still felt very weak so he crawled over to the locker he opened it and reached up to the pistol and managed to grab it despite it feeling impossible and he heard the woman on the intercom again "It doesn't have an energy cell worry about that later" He noticed the tanks next to the door about to explode and crawled behind a wall as they exploded, Deciding to try and stand he slowly got up and was barely able to put any weight on his legs so he leaned on the wall for support as he made his way out when he made it past the door he saw an energy cell on the floor he slowly got down and grabbed it and after a few seconds managed to figure out how to insert it

Turning the corner he spotted a mech take aim at him, Shepard raised the pistol and after a couple of missed shots managed to hit it taking its head off

Making his way past the mechs he encountered he eventually he was able to stand and walk on his own without having to hold on to something

When he exited into a large open area he spotted someone under fire from mechs and ducked into cover with him "Shepard? what are you doing here"

"I just woke up you probably know more than I do"

"Right sorry about that, I'm Jacob Taylor head of sec-" But jacob was interrupted by a mech who fired a few shots towards Jacob who got up and used his biotics to flatten the mech against the wall "Tell you what commander help me with these mechs and I'll answer all the questions you want" Shepard showed his agreement with Jacob by shooting a mechs head off

After downing the last of the mechs Jacob got up and spoke "Alright I promised I'd answer you're questions so shoot"

"Where are we?"

"You're on board the Lazarus station home to project Lazarus"

"Whats the Lazarus project exactly?"

"I don't know the specifics but in short it was meant to bring you back to life seems to have worked considering when I first saw you, you were nothing back a charred body"

"What happened to my crew?"

"Aside from Pressly and a dozen others casualties most of the crew survived but as for where they are now is anyones guess" Suddenly the radio came to life "Check, Check is anyone on this frequency"

"Wilson this is Jacob where are you"

"Server room B I need help the mechs are keeping me pinned hurry"

"Roger that Wilson stay on this frequency" Shepard and Jacob headed out towards the Server room to find Wilson

After destroying a couple of other mechs they found him "Bastards got me in the leg" Shepard applied some medi gel to his wound and he got up "Well this went to hell quick" Jacob spoke "Where's Miranda?"

"Last I heard she was over in the other wing which is swarming with mechs so chances are she's dead"

Shepard was getting annoyed by all this "You're all strangers to me and right now all I care about is getting off this station" Some mechs entered and before they could even raise their weapons Shepard shot the fuel containers and the mechs were vaporized in the explosion

Shepard walked forward a bit before jacob spoke again "Okay this is getting tense Shepard if I tell you who we work for will you trust us" Wilson scoffed "You really think thats a good idea"

"We won't get anywhere if we have guns pointed at each other" Jacob turned back towards Shepard "This station, The Lazarus project its all funded by Cerberus" Shepard crossed his arms and replied "I've wiped out my share of Cerberus ops when I was a spectre why would they want my help?"

"Those answers are way above my pay grade Shepard" Shepard turned around and continued to speak "I don't care what you say Im not working with terrorists!"

They continued on in silence towards the hangar bay where they encountered a few more mechs but as before they were quickly dropped as they were only programmed to walked forwards and shoot blindly

reaching the door to the dropships Wilson rushed forwards and deactivated the lock but was shocked when he saw someone he was hoping had died "Miranda?! but you're supposed to be-" Wilson didn't get to finish his sentence as Miranda raised her sidearm and fired putting a laser shot right between his eyes and Miranda spoke finishing off Wilson's sentence "Dead?"

Jacob rushed forward "What the hell are you doing?!" Miranda looked at him and replied cooly "My job Wilson betrayed us all" Shepard lowered his weapon "If you say so, Whats our next step"

"We get on the dropship and go, My boss wants to speak with you"

"You mean the Illusive man? I know you work for cerberus" Miranda turned back to Jacob and spoke "Ah Jacob I should have known you're conscience would get the better of you" Jacob replied "Lying to the Commander Isn't the way to get him to join our cause"

"Well since were getting everything out in the open is there anything else you want to ask before we go Commander?" Shepard shook his head "No I just want to get off this station"

"Alright lets go then" The three of them boarded the Condor dropship in the hanger and left the station

En route to secondary Cerberus station

Shepard was looking starring at the ceiling before Miranda spoke to him "Before you meet the Illusive man we need to run a few tests to evaluate your condition" Jacob spoke "Come on Miranda more tests? Shepard took those mechs down without any trouble that has to be good enough"

"Its been two years since the attack, The Illusive man needs to know that Shepard's personality and memories are intact ask the questions" Shepard was shocked at that last statement "Did you say two years? I've been gone that long?

Jacob spoke as he brought up his Omni tool "Two years and twelve days and you were on an operating table for most of it. Okay records show you were a spacer kid raised mostly on one ship or another, You enlisted and won a medal fighting Batarians in the Skyllian Blitz do you remember that"

"A lot of lives depended on me holding that position I did what I had to and its the reason I was recruited into the Spartan branch"

"However you want to put it, it was damn impressive, I had friends who were there, Satisfied Miranda"

"Almost lets try something more recent, Virmire where you destroyed Sarens cloning facility you had to leave one of your squad behind to die in the blast"

"1st Lieutenant Kaiden Alenko was killed in action it was your call why did you leave him behind"

Shepard still felt very guilty over that decision "I left a friend to die that day and I didn't do it casually but I had to save as many people as I could, Kaidan gave his life for the rest of the team, Without him I couldn't have stopped Saren, he died a hero"

"I understand Commander and I wasn't questioning your decision everyone at cerberus knows that facility had to be destroyed"

"Shepard think back to the citadel after the Fifth fleet saved the destiny ascension and you killed Saren what happend next?"

"Humanity was offered a seat on the council I recommended Ambassador Udina for the position"

"Yes ambassador Udina is now councilor Udina he's been doing alot on the Council to advance Human interests"

Jacob spoke"Still good to know the new councilor isn't putting politics ahead of defence"

"You're memory seems solid, There are other tests we should run-" But Jacob interrupted her "Come on Miranda enough with the quizzes the memories are there and I can vouch for Shepards combat skills"

"I suppose you're right, we'll have to hope the Illusive man accepts our little field test as evidence enough"

A couple of hours later the Condor reached the station and docked Miranda turned to Shepard "The Illusive man is waiting for you downstairs"

Shepard walked down the steps and stood in the middle of the room when a holographic grid rose and started scanning him when it was done he saw the Illusive man through the display "Commander Shepard"

"Illusive man I thought we'd be meeting face to face"

"A necessary percaution not unusual for people who know what you and I know"

"You might be the reason Im still alive but that doesn't mean I trust you"

"You need to put your personal feelings aside, Humanity is up against one of the greatest threats of our existance"

"The Reapers" The illusive man tapped his cigarette over his ash tray and continued "Good to see you're memory is still intact how are you feeling"

"You need to earn the right to ask me those kind of questions"

"Cerberus isn't as evil as you believe, You and I are on the same side we just have different methods"

"Cut to the chase what are the Reapers doing that made you bring me back"

"We're at war, no one wants to admit it but Humanity is under attack, While you've been dead entire human colonies have been disappearing, We believe it's someone working for the Reapers just as Saren and the Geth aided Sovereign, You've seen it yourself you bested all of them thats just one reason we chose you"

"It'll take a lot more than what you say to convince me I need to see evidence"

"I'd be dissapointed if you said otherwise, Go to Freedoms Progress the latest colony to be hit"

"Is this a volunteer job or am I beeing voulnteered"

"You always have a choice Shepard if you don't find the evidence we're looking for we both part ways" The Illusive man ended the transmission and Shepard seriously thought about just leaving but something told him that this was alot bigger than he thought so he went back upstairs and got his gear ready


	3. Chapter 3: Reunion and Answers

Shepard and the others got their gear together and piled into the Condor making their way to Freedoms Progress Shepard told them that the first priority was to find any survivors that they could hoping that someone might be able to give them an answer as to what had happened

After they landed they made their way into one of the nearby buildings and the lights flickered on as Jacob commented on what they were seeing "Looks like everyone got up and left right in the middle of dinner" they moved forward abit exiting into a courtyard and aside from it being deserted nothing was out of place "Strange no structural damage or signs of any firefights"

They continued on for a bit passing through a large door seperating the districts when they suddenly came under fire from security mechs and just like the ones on the space station they didn't really prove to be challenging as it only took a couple of shots to eliminate them "Those mechs shouldn't have fired on us they should have recognized us as human" Miranda joined in "Someone reprogrammed them, looks like there may be someone here after all"

Coming up on one of the prefab's Shepard heard talking coming from the inside he opened the door and went in weapon drawn and when the people in the corner of the room heard the door open they drew their weapons "Stop right there!" but one of the Quarians got in front of them "Prazza you said you'd let me handle this" She turned to face the people who entered and was shocked by who she saw "Wait, Shepard?" Shepard immediatley recognized Tali and ordered the others to lower their weapons and Prazza spoke again "Im not taking any chances with Cerberus operatives!" Tali glared at him and shouted "Put those weapons down!" she turned back to Shepard and asked "Shepard is that- You're alive?" Shepard knew just how to assure her it was him "Remember those shield specs I gave you Tali? did it help you complete you're pilgrimage?"

"Yes it did, Prazza weapons down this is definitley Commander Shepard" He put his weapon away and spoke "Why is you're old Commander working for Cerberus?"

"Maybe we should ask"

"Cerberus rebuilt me but I'm not taking their orders we can discuss specifics once I know why you're here"

"One of our people was here on Pilgrimage. His name is Veetor and we came to find him"

"If Veetor survived the attack maybe he can tell us what happened to this colony"

"Thats the hope we've seen him but he might not be in the best state to answer questions he was injured and ah nervous-" Prazza interrupted her "She means that he's unstable combine with the damage to his CO2 scrubbers and an open air infection he's likely delerious" Tali continued "Last we saw he was in a warehouse on the far side of the settlement we think he's also reprogrammed the colony's security to attack anyone on sight"

"Veetors the only one who can tell us what happened here we should work together to find him" Prazza scoffed "Now were working with Cerberus?" Tali shot him another glare "No Prazza you're working for me if you don't like it you can go keep the ship warm" After working out a plan the two teams split up and made their way down to the warehouse

Encountering a couple of rocket and aerial drones they made their way down a bit further when Tali radioed in "Shepard, Prazza and his squad rushed on ahead I told them to wait but they wouldn't listen, They want to find Veetor and take him away before you get here!"

They made their way to the warehouse door and Shepard ordered Miranda and Jacob into cover by the door while shepard got behind a concrete divider in front of it when they were in position Tali warned him that Veetor reprogrammed a heavy Mech and opened the door

They rushed inside when the door opened and saw the mech massacre the Quarian squad once they were in cover Shepard got out a grenade and told the others to distract the mech while he made his way around behind it

With the mech distracted Shepard got behind it no problem and when he managed to get close enough he stuck his grenade to it and ducked for cover, A second later it detonated taking the mechs head off and knocking the rest of the body over onto its side

Regrouping Shepard and the others entered the building where Veetor was and saw him sitting in front of a dozen screens "Monster's coming back, mechs will protect safe from swarms have to hide no monsters no swarms, no no no no no" Shepard walked forward slowly and spoke "Veetor?" he replied "No Veetor. Not here. Swarms can't find. monsters coming have to hide"

"Nobodies going to hurt you anymore" Jacob spoke "I don't think he can hear you commander" as Veetor kept rambling Shepard activated his omni tool and brought it up deactivating the monitors which seemed to snap him out of it as he got up from his chair "You're human, Where did you hide? How come they didn't find you?"

"Who didn't find us?"

The...The monsters. The swarms they took everyone"

"Why didn't the colonists fight back Veetor? What happened" Veetor turned back to the monitors "You don't know you didn't see. But I see everything" He activated the monitors revealing security footage and as they watched they saw large insects flying around and when the camera zoomed in on one of the aliens Jacob spoke "What the hell is that?

While the others may not have known what they saw Miranda did "My god I think its a collector"

"What are the Collectors doing here? they usually have merenaries do their work for them" Miranda nodded "Guess we'll have to find out won't we"

"The collectors have advanced technology, They could have a weapon that disables an entire settlement at once" Veetor spoke "The seeker swarms, no one can hide the seekers find you freeze you then the monsters take you away, The monsters took the people onto the ship and then they left, But they'll be back for me no one escapes!"

"I think thats all we'll be able to get out of him commander" Veetor continued "I studied them, The monsters, The swarms I recorded them lots of readings, Electro magnetic, Dark energy" Miranda joined in "We need to get this data to the Illusive man grab the Quarian and call the dropship for a pickup" Tali entered overhearing what Miranda said "What? Veetor is injured! He needs treatment not an interrogation!"

"You're people tried to betray us once already if we give him to you we'll never get what we-" Shepard cut her off "Shut it Lawson, he's traumatized and needs medical care he goes with Tali all we need is the data so grab that instead" Miranda glared at him but decided not to press the issue any further

"Thanks Shepard nice to know Cerberus hasn't changed you"

"Good seeing you Tali take care of yourself" They grabbed the data and left

Back on the Station

Shepard headed back down to comm room to talk to the Illusive man

"Shepard good work on Freedom's Progress, The Quarians forwarded their findings from Veetors debriefing no new data but a surprising olive branch given our history, You and I have different methods, but I can't argue with the results" Shepard just shrugged "You ever think about playing nice once in a while? You know as in not painting all aliens as though they were part of the Covenant"

"Diplomacy is great when it works, but difficult when everyone percieves you as a threat, But more importantly, you confirmed the Collectors were behind the abductions" Shepard rolled his eyes "Yeah I get the feeling you knew about their involvment" Illusive man continued "I had my suspicions but needed proof the Collectors are enigmatic at best, They periodicly travel to the Terminus systems for seemingly unimportant things or specimens usually in exchange for technology once they've completed their transactions they disappear"

"Why the interest in humans though"

"It could be because we developed our technology and evolved outside the Reapers plans we have technology they likely never encountered or it could be because of you we don't know for sure, But what really concerns me is why bother abducting the colonists when their paralyzed instead of simply killing them"

"You're holding something back, How do you know the Reapers are involved"

"The patterns are there, buried in the data, the council and UEG want to believe the threat is over but you and I know better, I won't wait until the Reapers are on the march we need to take the fight to them"

"If this is a war I'll need an army or a really good team" The Illusive man brought up a display "I've already compiled a list of soldiers, scientists and mercenaries, you'll get dossiers on the best of them"

"Keep you're list I want people I trust the ones who helped me stop Saren and the Geth"

"That was two years ago Commander most of them have moved on...or their allegiances have changed

"Where's Urdnot Wrex"

"He returned to Tuchanka and hasn't gone off world in 18 months, he's trying to unite the Krogan clans

"What about Tali she helped us on Freedoms Progress"

"That was unexpected I'll need more data before I commit to that"

"Liara T'Soni?"

"She's on Illium my sources say she's working for the Shadow Broker if so she can't be trusted"

"Where's Garrus Vakarian"

"The Turian disappeared shortly after your death even we haven't been able to track him down"

"Where's Gunnery Sergeant McCall"

"Master Sergeant McCall is still in the Marines, He was reassigned to a special ops unit after the Normandy was destroyed"

"Where's Ashley Williams"

"Also still in the Marines her file is surprisingly well classified" Shepard sighed "Okay I get it their not available, You worry about the Collectors I'll make sure my teams ready"

"Good, two things before you go: First head to omega and find Mordin Solus. He's a brilliant Salarian scientist, our intel suggests he may be able to counteract the collectors paralyzing swarms"

"All right whats the other thing?"

"I found a pilot I think you might like I hear he's one of the best someone you can trust"And The Illusive man ended the transmission

Shepard turned around hearing a familiar voice "Hey Commander just like old times huh?"

Back upstairs "I can't believe its you Joker"

"Look whos talking I saw you get spaced"

"Got lucky with a lot of strings attached, how'd you get here"Heading up a flight of stairs Joker continued "It all fell apart without you Commander, everything you stirred up the council just wanted it gone, Team was broken up, records sealed and I was grounded, The Navy took away the one thing that mattered to me, hell yeah I joined Cerberus"

"You really trust the Illusive man?"

"I don't trust anyone who makes more than I do. But they aren't all bad saved your life let me fly, and there's this, they only told me last night"

As they looked out the window the lights in the hangar slowly activated one at a time until they fully revealed a ship Shepard once used in the fight against Saren "It's good to be home huh commander?"

"Guess we'll have to give her a name"

Codex: Timeline 2583-85

July 6th 2583: The UNSC Normandy is attacked by unknown hostiles and is destroyed while most of the crew escape Commander Shepard is Killed in Action

July 19th 2583: Commander Shepard's body is recovered by Cerberus for Project Lazarus

July 27th 2583: The Funeral of Commander Shepard is held in Vancouver during a small private ceremony attended by most of Shepards squadmates and his family

September 2583: The UNSC begins refitting most of its forces with new energy weapons that have been in R&amp;D for years

October 2583 The Normandy crew is broken up and reassigned to various postings

January 2584: First exchange program between the UNSC and Turian Military begins with Turian Soldiers taking part in ODST training and UNSC Marines being assigned to Turian patrols near the Terminus systems

February 2584: Last known sighting of Garrus Vakarian on Palaven

March 18th 2584: Attempted assassination of Lieutenant General Anthony McCall who is being considered for head of the Joint Chiefs by Cerberus who was grooming VADM Hardins for the position to advance their agenda

April 2584: First Human colony disappears

May 2585: The first Turians to take part in ODST training pass the course describing it as absolute hell and would rather face a thousand Krogan charging them then repeat the course

July 2584: One year celebration of the battle for the citadel takes place

December 2584: General Anthony McCall is announced as new Chairman of the Joint Chiefs and promoted

March 2585: 10th human colony is hit with no explanation as to how everyone simply vanished

July 19th 2585: Current date


	4. Chapter 4: Archangel

Shepard and the others boarded the Normandy walking into the CIC of the ship Shepard looked around and aside from some visual and tech upgrades it looked exactly the same as the first Normandy, Joker was already in the pilots seat and the ship departed the station in the center of the CIC Miranda spoke to Shepard "We know the collectors use swarms to paralyze people so we should get Professor Solus first since his expertise will come in handy" A synthesized voice came in over the intercom "Accquiring Professor Solus seems a logical step" Shepard looked up "Who are you" an Image appeared behind him, It was a Blue sphere and spoke "I am the Normandy's Enhanced Defence Intelligence or EDI"

"Helmsmen aren't happy when someone else takes control of the ship especially an AI"

"While that is one of my functions I will leave the piloting of the vessel to Mr Moreau" EDI's avatar disappeared and the others had already gone to their stations Shepard went to the cockpit and Joker turned around "Can you believe this Commander? its my baby! better than new! it fits me like a glove! And leather seats, military may set the hardware standard but on a first gen frigate they could care less if the seats breathe. Civillian sector comfort by design" EDI spoke "The reproduction is not intended to be perfect Mr Moreau seamless improvements were made" Joker sighed while he worked well with Achilles Shepard noticed something about EDI irritated Joker, maybe it was the fact the EDI lacked the sense of humor Achilles and other AI's had "And theres the downside. I liked the Normandy before now she's got this thing I don't want to talk about its like ship cancer"

"I don't like it either but were stuck with it"

"Until I find a soldering gun there's got to be some wires I can cross to make it hurt"

"No sabotage or I let the AI take the helm"

"Alright, Alright don't break the bosses toys got it"

Shepard left Joker and met a couple of the crew such as his Yeoman but also caught up with doctor Chakwas before heading up to his quarters, when he entered he saw a large room with a fish tank, display cabinet, desk with a personal computer and a large king sized bed and L shaped couch in front of it he went over to his terminal and looked through his messages one of them was from Anderson asking him to come to the citadel and meet with him on the off chance the rumors of him being alive were true, it had barely been a few days and already there was speculation on whether or not Shepard was in the land of the living again

After checking the messages he decided to catch up on what has happened in the last couple of years and went through the historical archives Cerberus had, he ran through the events and while alot of it was relatively mundane a few events had piqued his interest such as the Council had now repealed the AI ban and was allowing new AI research in council space mostly headed by the UNSC since we have the most experience of any race with them other developments were the massive overhaul of the UNSC arsenal to energy weapons the most recent development being the MAC's used by the Navy and on ODP's were being replaced with Particle Accelarator Cannons but the biggest concern was tensions with the Batarians were rapidly approaching the breaking point and after Shepard's death war nearly broke a few times, The strangest thing he read was that Udina and the UEG were pushing for the council to aid the Migrant fleet probably owing to the fact that a Quarian helped stop Saren and while the UEG is the only one providing aid currently their is discussion among the council about it

After finishing at his terminal he ordered that a course be set for the Omega space station, which was the unofficial capital of the Terminus systems since the most powerful people in the Terminus were based there the people he was picking up from there were Zaeed Massani an who was Marine special forces before turning mercenary and was rumored to be the best in the Terminus, Mordin Solus the scientist was a former Special Tasks Group operative, And finally Archangel not much was known about him aside from him likely being a Turian and managing to piss off every major merc band in the Terminus systems

Arriving at the station a few hours later Shepard and the others disembarked onto Omega and were greeted by a Batarian "Well now this is a suprise the famous Spartan Commander Shepard back from the dead"

"You know who I am?"

"We had you tagged the second you entered the Terminus systems your not as covert as you think, Aria wants to see you in Afterlife, word of advice don't keep her waiting" he turned and left, Just down the hall Shepard saw Massani beating someone

"Are you Zaeed Massani?" he turned to face Shepard and saw one of his eye's was dead "Yeah that's me you must be Shepard, heard alot about you" the Batarian he was beating tried to say something but Massani hit him again "I don't suppose Cerberus told you about the job I picked up before they approached me did they?" Shepard rolled his eyes of course he would have to handle this "Why am I not suprised alright we'll handle it in the mean time welcome aboard you can go set up on the ship" he nodded grabbing the Batarian and dragging him along to what Shepard assumed was a meeting place he was taking him to but he didn't really concern himself with it

Heading through the door into Omega proper Shepard and the others exited into a wide open area and thought if the citadel had an ugly twin Omega was it

Directly ahead of the group was the club the Batarian mentioned Afterlife, they walked up to the door and the bouncer spoke to them "Go on in Aria's expecting you" they entered into a large area that had a holographic display in the middle of the room, They saw a balcony overlooking the bar and headed up it figuring that was where Aria was when they reached the steps just behind Aria her guards drew their weapons and aimed while one of them got a scanner out "Stand still" he began scanning Shepard who grabbed his pistol "If your looking for weapons your not doing a very good job" Aria spoke "Can't bet too careful with dead spectres especially one that's a spartan" the guard put the scanner away "Their clean" he stepped aside and Aria sat down "I only have one rule here on Omega but its fairly simple to remember, Don't. Fuck. With Aria"

"Easy enought to remember"

"Good but if you forget my guards will remind you" The Batarian picked up "Then I toss your sorry ass out the airlock" Shepard glared at the Batarian "I'd like to see you try, considering I only need my thumb to crush your windpipe" The guard shut up after that and Aria spoke "So what are you doing on Omega anyway?"

"I'm looking for people to recruit for a mission, I'm told you know where to find them"

"Depends on who they are"

"Where can I find Mordin Solus"

"He's running a clinic in the lower levels of the station but getting to him is the hard part, the lower levels have been hit by a plague and we had to seal that part of the station off, But if your after him I tell the guard to let you through"

"Okay how about Archangel I heard he's also on the station"

"With every major merc organization after him, He's pissed them off so much they banded together to take him down, but he's held them off so far, Talk to the Merc recruiting station just downstairs they'll tell you where he is" Shepard got up and left he decided to get archagnel first considering the number of merc's he had breathing down his neck

They went to the recruiting station and the recruiter spoke "You three look like you could do some damage, You interested?"

"If this is the place to go after Archangel"

"It is, standard fee is 500 credits each you get paid when the jobs done, you have to bring your own equipment, looks like your covered for that, And no this doesn't make you a member of the Blue suns, eclipse or Blood pack, your a freelancer thats it, alright head out to the shuttlepad we've got a guy waiting there to point the way for you" They got the info and left

Once they got on a shuttle they quickly arrived at their destination and were greeted by another Batarian "I hope your ready Archangel's been annhilating you freelancers"

"Just point us where to go"

"Go meet up with Sergeant Kathka near the barricade he'll tell you what you need to do"

Shepard and the others made their way through the mercenary camp, EDI advised sabotaging the heavy mechs and gunship to make escaping the area easier

As they moved they saw preparations being made for a massive attack Shepard found it hard to believe that one Turian could cause so much trouble for the three biggest merc bands in the Terminus

After reprogramming the heavy mech's IFF system Shepard found Sergeant Kathka "So your the freelancers I was told to expect"

"Kathka?"

"Yeah you and your friends here are going in with some other freelancers to try and destroy some of Archangel's defences and keep him busy while we get our forces into position to take him by surprise" Once he was done speaking Kathka's terminal beeped "Well that's your cue to go, I've got to get this gunship back up to 100% before my boss decides its needed again" Shepard approached Kathka from behind and put him in a choke hold, Kathka tried to pry Shepard lose but eventually stopped moving all together passing out, Shepard moved his body out of sight and went over the barrier to join the fight

Once over on the other side the team stayed behind the freelancers silently picking them off one at a time as they made their way forward using the freelancers focus on archangel to their advantage

Once they made it to the door leading to Archanagels position Shepard approached the technician trying to get inside with his bayonet out, Shepard got in close put his hand over the tech's mouth and stuck the knife in his back waiting a couple seconds to make sure he would stay down

Once that was done Shepard and the others went into the room weapons raised upon seeing Archangel Shepard spoke "Archangel?" Archangel didn't respond he just waved for them to wait a moment before firing off a shot taking out a merc behind cover before walking over taking off his helmet and sitting down revealing someone Shepard didn't expect to see on Omega, Garrus Vakarian

"Shepard, I thought you were dead"

"Garrus! What are you doing here"

"Im on assignment" Shepard raised an eyebrow at that "Assignment?"

"Yeah, Im here on Omega to try and disrupt the mercs leadership in case you haven't heard merecenary raids in council space have become more organized in the last couple years so Im here to try and cause as much damage to them as possible"

"I take it that means you're a spectre now?"

"Yeah took a while but my working with you against Saren helped got inducted just over a year ago" Shepard decided to get back on track "Well we managed to get here but getting out isn't going to be easy"

"No it won't that bridge has saved my life, funneling those idiots into scope, but it works both ways, They'll slaughter us if we try to get out that way, this place has held them off so far and with the three of you, I suggest we hold this location wait for a crack in their defences, and take our chances, Its not perfect but its all we got"

Shepard had another idea "you stay up here, Jacob you got any explosives with you?"

"Plenty, Why?"

"Go rig the bride supports but don't detonate until I tell you, Once that's done you and Miranda head to the basement and rig the tunnels" Garrus turned to face Shepard "What do you have in mind?"

"I managed to get the mercs plans while I was in their base, freelancers were the first wave, Eclipse and mechs are the second, the blood pack are moving in through the sublevel at the same time as eclipse is crossing the bridge, the final wave is the blue suns dropping in by gunship, We hold eclipse at the bridge and wait for the blood pack to move into the tunnels, once there we blow the bridge and collapse the access tunnel's taking the two groups out in a single strike, making things easier for us when we have to face the blue suns"

"But how are we going to get out?"

"My ships AI will hack a shuttle for us to take once the mercs are taken care of"

"Okay that'll work all we need to do now is wait" Miranda and Jacob returned "Charges are set and ready to blow" Shepard and Garrus set up at the balcony while Miranda and Jacob got set up at the entrance

After a few minutes Eclipse forces started moving across the bridge and dropped their mech "Hold fire the mech will take care of the initial wave" and sure enough the YMIR mech opened up catching the advancing mercs off guard managing to kill at least a dozen of them before the mech was destroyed

More eclipse forces started moving in and the team opened up on them keeping them at the bridge and waiting for the motion sensor's in the tunnels to tell them that the blood pack were moving in

A few minutes later Shepard's omni tool went off the blood pack were moving in now in significant numbers "Jacob blow the charges" Jacob did so and explosions rocked the compound as Eclipse mercs dropped to their doom and blood pack forces were crushed in the tunnels

Once they made sure it was clear everyone regrouped upstairs "Only the blue suns are left I say we take our chances and get out now"

"Yeah Tarak's got the toughest group but we should be-" Garrus was unable to finish his sentence as a gunship appeared to the side of the building "Archangel!" The gunship opened fire hitting Garrus and wounding him badly

Shepard and the team opened up on the gunship but because it wasn't fully repaired it had a hard time moving

After a few minutes of sustained fire the gunship went up in flames, Once the area was clear Shepard went over to check on Garrus who let out a pained gasp "Garrus!" He got the medical supplies out and started treating the wounds, he looked over to Miranda "Get us that evac now!"

12 hours later, Normandy briefing room

Jacob was giving Shepard an update on Garrus' condition "Shepard Chakwas did what she could for Garrus, surgical implants and such but we're not entirley sure what his status will be" But when the door opened Shepard got the answer he had hoped for "Huh, tough bastard, didn't think he'd be up yet"

Garrus entered the room and spoke "No one would give me a mirror how does it look"

"Hell Garrus you were always ugly, slap some face paint on and your good as new" Garrus laughed "Ow, don't make me laugh my face is barely holding together as is" Jacob left and Garrus continued "Frankly I'm more worried about you, Cerberus, Shepard? You remember those experiments they had going?"

"Which is why Im glad your here Garrus If Im walking into hell, I want someone I trust at my side"

"You realize this plan has me walking into hell too, just like old times, Im fit for duty whenever you need me Shepard I'll settle in and see what I can do at the forward batteries" Garrus turned and left, Shepard decided to see if anything had happened while he was on Omega but it was still about the tensions in the Verge with the Batarians and how things were about to blow up, deciding there was nothing else to do Shepard went to his bed to get some sleep before heading back to Omega for Mordin Solus

Codex: Batarian Cold War

Ever since humanity made first contact with the Council relations with the Batarian Hegemony have been Icy at best due to the Batarians practicing slavery the UEG kept its distance relations between the two didn't become hostile until 2546 when the Batarians launched slave raids on human colonies, while these raids failed it infuriated the UEG and council that the Batarians would do this while a Galactic war was happening, One the Batarians stayed out of hoping the Council and UEG would be destroyed, in response to this the UNSC sent prowlers with nuclear weapons into Batarian space destroying several fleets and shipyard, while the raids stopped for the remainder of the war tensions escalated

in 2570 Batarian slavers attacked the colony of Mindoir another raid that failed but it was the Skyllian Blitz that nearly started a massive war when the attack failed the UNSC launched a crushing counter attack at Torfan sending in several companies of marines to destroy the slaver bases there and once again the Batarians responded with threats of war but didn't do anything

After the Council refused to declare the Verge Batarian territory they withdrew from the Citadel and began to activley seek war with humanity building up its forces for such a war

Since the end of the Geth war tensions have escalated dramatically with Batarian ships violating UEG space and trying to goad any UNSC ships they encounter into firing and as of 2585 many are concerned that the cold war will go hot before the years end, Though many doubt the Batarians would win a war considering the UNSC has the second largest fleet in the galaxy, high end energy weapons and the full backing of the citadel council meaning any war that occurs will undoubtedly result in a UNSC victory


	5. Chapter 5: The Scientist

A few hours after getting back to the ship Shepard and the others headed back onto Omega to get Mordin Solus who was in a plague ravaged part of the station, Apparently the plague hitting the station affected every race aside from Humans and Vorcha so Shepard decided to only take Jacob and Zaeed with him as he didn't want to risk exposing Garrus to any disease

Once they made it past the security checkpoint they found that for the most part the area was abandoned but they did see bodies being burned in the street, Zaeed spoke "Plague control 101 burn the bodies before they can spread the disease" The team continued on for a bit when they noticed Blood pack mercs in what was thought to be blue suns territory, the mercs were distracted so Shepard and Jacob took them out quietly before they could alert anyone else "Blue suns have given up alot of turf, that doesn't bode well for them" Zaeed shrugged "Well considering that alot of blue suns are Turians and Batarians they don't have much choice if they're losing men to the black plague"

The team moved on eventually coming across a med clinic, Shepard went to the receptionist "Is there a Salarian named Mordin Solus here?" the receptionist looked up "Doctor Solus is just inside, but don't disturb the paitents"

Heading inside Shepard saw alot of people who were hit by the plague some looked worse than others and didn't seem like they would last another hour in their current state

Moving through the clinic Shepard caught sight of a Salarian in one of the rooms down the hall and decided to check if it was Solus

Shepard approached and spoke "Professor Mordin Solus?" The Salarian didn't say anything at first he just approached and waved his omni tool before speaking "Hmm don't recognize you from area, too well armed for refugees, no mercenary uniform, Quarantine still in effect" he walked over to his terminal "Here for something else. Vorcha? Crew to clean them out? Unlikely Vorcha a symptom not a cause, The plague? investigating use as possible bioweapon? no too many guns not enough data equipment, soldiers not scientists" Shepard decided to end the speculation there "Relax Mordin, I'm Commander Shepard and I came here to find you, Im on a critical mission and need your help"

"Mission? what mission? No too busy clinic understaffed plague spreading too fast who sent you?"

"Ever heard of an organization called Cerberus?"

"Crossed paths on occasion, designated terrorists by UEG and Council, but thought they only worked with humans, why request Salarian aid"

"Im on a mission to shut down the collectors and I need youur help"

"Collectors? interesting plague hitting these slums engineered, collectors one of few groups with technology to design it, our goals may be similar, But must stop plauge, already have a cure need to distribute it at environmental control center, Vorcha guarding it need to kill them"

"I'll get in and deal with the Vorcha"

"One more thing Daniel, one of my assistants went into Vorcha territory looking for victims hasn't come back"

"I'll keep an eye out for him, Lets move"

Once they had the cure they moved out to their destination upon exiting the clinic they drew their weapons and made sure the energy cells were fully charged

As they rounded a corner they found a couple of Vorcha, Shepard and Jacob managed to sneak up behind them, While Jacob placed one in a chokehold Shepard got his bayonet out and stabbed the Vorcha he had in front of him, but any chance of finishing their op quietly was ruined when some of their friends appeared and opened fire on them but Shepard managed to drop them quickly

As they got closer to the enviromental controls they heard shouting "Don't lie to me! We know your spreading the plague human don't try to convince me otherwise" Shepard entered the room weapon raised the Batarians raised their weapons as well "Don't come any closer or he dies" Shepard spoke to defuse the situation quickly "I know your scared of the plague but this man isn't to blame for it, If he was spreading the plague why would he come into Vorcha territory their immune" one of the Batarians spoke "He's right it doesn't make any sense" the leader lowered his weapon "If we release the prisoner can we go?"

"Yes" The leader nodded to the other two and they left without another word

Shepard freed their prisoner from his restraints "You Daniel? the Professor asked me to keep an eye out for you"

"Yes I am and thanks for your help"

"You get back to the clinic we'll take care of the cure"

A few minutes later they arrived at the envriomental controls and the Vorcha in the room immediatley opened fire but they didn't last long as the team managed to take them out fairly quickly

Once the cure was inserted into the enviromental system it dispersed throughout the quarantine zone

With their mission complete the team went back to the clinic and met with Mordin

"Airborne enviromental systems engaged, Viral levels dropping, paitents improving, Vorcha retreating, well done Shepard, Thank you"

"Now that the plague is dealt with can you come with me?"

"Yes just need to wrap a few things up here will meet you on ship"

1 hour later, conference room, Normandy

Shepard was in the conference room when Jacob escorted Mordin in "Welcome to the Normandy professor, its an honor to have you on board"

"Yes very exciting Cerberus working with aliens, unexpected. Illusive man branching out, maybe not so human centric?" Shepard walked over to the professor and spoke "Don't kid yourself professor Humans still come first in his eyes but alot of human colonies have been vanishing and we need help" Jacob took over

"There is virtually no evidence that anything unusual has happened at all expect that every man woman and child is gone" Shepard continued "And you don't have to guess about what happened we gathered samples from one of the colonies analyze them and find out how the collectors did this"

"Yes of course analyze the samples going to need a lab" EDI chimed in "There is a fully equipped lab on the combat deck if you find anything lacking please place a requisition order"

"Ah yes AI used on human ships extensivley very helpful" Jacob walked over "Follow me professor the lab is this way" With that they left the room

Shepard decided to head to the cockpit and found the Joker and EDI weren't bickering at the moment, Joker turned his chair around "Commander? What can I do for you?"

"You keep in touch with any of the old team"

"For a bit yeah but after the original Normandy was destroyed we all kind of drifted apart, haven't heard anything from Ash in over a year now and I haven't seen McCall since your funeral, We were your team commander without you it all just fell apart"

Shepard decided to leave it at that and went down to see Garrus "Shepard anything I can help you with"

"Seem to be getting familiar with the main gun"

"Yeah well if we ever go up against a collector ship their won't be much left of it these aren't the mini MAC's the original had their Particle cannons very powerful ones" Shepard decided to change the subject "So how did you get to be a spectre anyway?"

"Well my work with you against Saren helped caught their attention and after a few missions under their observation they made me a Spectre"

"Any interesting ops"

"Yeah none like what we went up against but I can't exactly talk about them you already now the op I was running on Omega"

"You hear anything from the old team?"

"Not much caught up with Ash a few months ago she seemed to be doing good before you ask, I haven't seen Liara since I left, Wrex is on Tuchanka though you probably already knew that headbutting every chieftan there is no doubt, I did run a few ops with McCall but again can't really talk about those" Shepard nodded and decided to leave "Well have fun calibrating the guns"

Before going to sleep Shepard had EDI set a course for the Citadel to see what Anderson had been up to and if he could get any Council support for his mission but his connection with Cerberus would make that difficult

**Sorry for the delay and the short chapter but haven't had a lot of time to write lately**


End file.
